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metabolomics-workbench-database

Query the Metabolomics Workbench REST API for metabolite structures and study metadata.

52|6|Updated Nov 24, 2025
Search Tags:#metabolomics#biomarker discovery#mass spectrometry#scientific data#RefMet#metabolite research#NIH database
One-click install
npx skills add https://github.com/ovachiever/droid-tings --skill metabolomics-workbench-database-ovachiever
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/ovachiever/droid-tings/tree/main/skills/metabolomics-workbench-database
Command: npx skills add https://github.com/ovachiever/droid-tings --skill metabolomics-workbench-database-ovachiever

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes references (resource) components.

What problem does it solve?

This skill automates access to the vast NIH Metabolomics Workbench database, eliminating manual data retrieval and nomenclature standardization. It streamlines metabolomics research, biomarker discovery, and data integration, saving scientists valuable time and reducing data processing complexity.

Core Features & Use Cases

  • Metabolite Data Retrieval: Query structures, identifiers, and classifications for over 4,200 studies, accelerating compound identification.
  • Study Metadata & Results: Access experimental details, factors, and complete datasets for metabolomics research, enabling rapid data exploration.
  • RefMet Standardization: Automatically standardize metabolite names and classify compounds for consistent analysis, ensuring data comparability.
  • Mass Spectrometry Search: Identify potential compounds by m/z values, ion adducts, and tolerance levels, streamlining MS data interpretation.
  • Use Case: Quickly find all human blood studies related to 'diabetes' that measure 'glucose' using LC-MS, then retrieve the full experimental data for further analysis, all through simple API calls.

Quick Start

Find all metabolomics studies in the NIH Metabolomics Workbench database that contain 'glucose' measurements.

Frequently Asked Questions about metabolomics-workbench-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I programmatically access metabolomics data from the NIH Metabolomics Workbench?▼

Programmatic access to metabolomics data is enabled through the Metabolomics Workbench REST API, which exposes study metadata, metabolite structures, and MS/NMR datasets. Query by identifier type (PubChem CID, InChI Key, HMDB, KEGG, RefMet) or m/z values with configurable mass accuracy and adduct settings to retrieve results in JSON or mwTab formats.

Can I search mass spectrometry data by m/z values across the Metabolomics Workbench?▼

Yes, mass spectrometry search queries m/z values with configurable ion adducts and tolerance levels to identify potential compounds. Results return matching metabolite structures and identifiers, streamlining MS data interpretation and compound identification in metabolomics workflows.

How do I standardize metabolite nomenclature across multiple studies?▼

RefMet standardization automatically normalizes metabolite names and classifies compounds for consistent analysis across studies. This ensures data comparability when integrating results from different experiments or databases within your metabolomics research.

What identifier types does the Metabolomics Workbench support for metabolite lookup?▼

Metabolite lookup supports multiple identifier standards: PubChem CID, InChI Key, HMDB, KEGG, and RefMet nomenclature. This enables flexible querying whether you have legacy identifiers or need to cross-reference compounds across biomarker discovery and metabolomics databases.

Can I retrieve complete experimental datasets and study metadata for biomarker discovery?▼

Yes, study metadata queries return experimental details, factors, and complete datasets for over 4,200 metabolomics studies. This enables rapid data exploration and integration for biomarker discovery, enabling targeted analysis without manual retrieval from the NIH database.

Does the API support multiple output formats for metabolomics data?▼

The REST API returns results in both JSON and mwTab formats, accommodating different downstream analysis workflows and data processing pipelines in metabolomics research and biomarker discovery applications.

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